I think that the most simple solution to the Tau-31 route is to make MacDuff farther away. Make it a 2 minute or 3 minute run instead of one. It both lowers profit margins to make other routes more competitive and also gives pirates plenty of time to waste the traders.
That would be a very very minimal change that would have a huge effect. I've done the math on 31. Its just a bit better than say Cam->Corfu->Cam Station but only because its less than 2km from each destination. Make that 5km and suddenly you got a different ball game.